Add sample CSV data and update .gitignore

Remove broad data-ignore rules from .gitignore so CSVs are tracked and add three example datasets for R/RMarkdown: r-and-rmarkdown/data/clinical.csv, gene_expression.csv, and sample_clinical.csv. These small example files provide clinical and gene expression sample data for demos and analyses.

Author: ShixiangWang

.gitignore

@@ -44,15 +44,5 @@ venv/
 *.html
 *.pdf
 *.docx
-!slides/*.html  # Keep rendered slides
-
-# Data (large files)
-*.csv
-*.tsv
-*.xlsx
-*.rds
-*.rda
-*.RData
-!data/*.csv     # Keep small example data
 
 **/*.quarto_ipynb

r-and-rmarkdown/data/clinical.csv

@@ -0,0 +1,31 @@
+patient_id,age,gender,diagnosis,survival_months,tumor_stage
+P001,45,F,Lung Cancer,24,II
+P002,62,M,Colorectal Cancer,36,III
+P003,38,F,Breast Cancer,48,I
+P004,71,M,Lung Cancer,12,IV
+P005,55,F,Breast Cancer,60,II
+P006,49,M,Colorectal Cancer,30,II
+P007,67,F,Lung Cancer,18,III
+P008,42,M,Breast Cancer,54,I
+P009,58,F,Colorectal Cancer,42,III
+P010,73,M,Lung Cancer,8,IV
+P011,36,F,Breast Cancer,72,I
+P012,61,M,Colorectal Cancer,28,II
+P013,44,F,Lung Cancer,22,II
+P014,69,M,Breast Cancer,45,III
+P015,52,F,Colorectal Cancer,38,II
+P016,77,M,Lung Cancer,6,IV
+P017,41,F,Breast Cancer,58,I
+P018,56,M,Colorectal Cancer,32,III
+P019,48,F,Lung Cancer,26,II
+P020,64,M,Breast Cancer,50,II
+P021,39,F,Colorectal Cancer,44,I
+P022,70,M,Lung Cancer,14,III
+P023,53,F,Breast Cancer,62,II
+P024,46,M,Colorectal Cancer,34,II
+P025,68,F,Lung Cancer,20,IV
+P026,43,M,Breast Cancer,56,I
+P027,59,F,Colorectal Cancer,40,III
+P028,74,M,Lung Cancer,10,IV
+P029,37,F,Breast Cancer,68,I
+P030,63,M,Colorectal Cancer,26,II

r-and-rmarkdown/data/gene_expression.csv

@@ -0,0 +1,16 @@
+gene_id,sample1,sample2,sample3,sample4,sample5,sample6
+TP53,12.5,11.8,13.2,10.5,14.1,12.0
+BRCA1,8.3,9.1,7.9,8.7,9.5,8.0
+EGFR,15.2,14.5,16.1,13.8,17.2,15.0
+MYC,20.1,19.3,21.5,18.2,22.0,19.8
+KRAS,6.7,7.2,6.1,7.8,7.5,6.5
+BCL2,9.8,10.2,9.1,10.5,11.0,9.5
+CASP3,7.5,7.0,8.0,6.8,8.2,7.3
+CDKN2A,5.2,5.8,4.9,6.1,6.5,5.0
+ERBB2,11.3,10.8,12.0,10.0,12.5,11.0
+PTEN,8.7,9.2,8.1,9.5,9.8,8.5
+ATM,10.1,9.6,10.8,9.0,11.2,9.8
+CHEK2,6.9,7.4,6.5,7.8,8.0,6.7
+MLH1,7.8,8.3,7.2,8.6,9.0,7.5
+MSH2,8.4,7.9,9.0,7.5,9.5,8.2
+PIK3CA,13.5,12.8,14.2,12.0,15.0,13.0

r-and-rmarkdown/data/sample_clinical.csv

@@ -0,0 +1,21 @@
+patient_id,age,gender,diagnosis,treatment,survival_months,status
+P001,45,Male,Lung Cancer,Chemotherapy,24,Alive
+P002,52,Female,Breast Cancer,Surgery+Radiation,36,Alive
+P003,67,Male,Colorectal Cancer,Chemotherapy,12,Deceased
+P004,58,Female,Lung Cancer,Targeted Therapy,18,Alive
+P005,71,Male,Prostate Cancer,Hormone Therapy,30,Alive
+P006,49,Female,Breast Cancer,Chemotherapy,8,Deceased
+P007,63,Male,Lung Cancer,Immunotherapy,15,Alive
+P008,55,Female,Ovarian Cancer,Surgery+Chemo,42,Alive
+P009,69,Male,Colorectal Cancer,Surgery,20,Deceased
+P010,47,Female,Breast Cancer,Radiation,28,Alive
+P011,61,Male,Pancreatic Cancer,Chemotherapy,6,Deceased
+P012,53,Female,Cervical Cancer,Surgery,48,Alive
+P013,59,Male,Liver Cancer,Targeted Therapy,10,Deceased
+P014,44,Female,Breast Cancer,Chemotherapy,32,Alive
+P015,66,Male,Lung Cancer,Immunotherapy,14,Deceased
+P016,51,Female,Endometrial Cancer,Surgery,38,Alive
+P017,57,Male,Stomach Cancer,Chemotherapy,16,Deceased
+P018,48,Female,Melanoma,Immunotherapy,22,Alive
+P019,64,Male,Kidney Cancer,Targeted Therapy,26,Alive
+P020,56,Female,Breast Cancer,Surgery+Radiation,40,Alive